CompareSams with LENIENT_HEADER=true doesn't work
If you are seeing an error, please provide(REQUIRED) :
a) Picard version used: 2.18.25
b) Exact command used:
PicardCommandLine CompareSAMs script_A1_hisat2_alignments.sam shell_A1_hisat2_alignments.sam -LENIENT_HEADER true
c) Entire error log:
PicardCommandLine CompareSAMs script_A1_hisat2_alignments.sam shell_A1_hisat2_alignments.sam -LENIENT_HEADER true
ERROR: No more than 2 positional arguments may be specified on the command line.
USAGE: CompareSAMs [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CompareSAMs
Compare two input ".sam" or ".bam" files. This tool initially compares the headers of SAM or BAM files. If the file
headers are comparable, the tool will examine and compare readUnmapped flag, reference name, start position and strand
between the SAMRecords. The tool summarizes information on the number of read pairs that match or mismatch, and of reads
that are missing or unmapped (stratified by direction: forward or reverse).
Usage example:
java -jar picard.jar CompareSAMs \
file_1.bam \
file_2.bam
Version: 2.18.25
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
If not an error, choose a category for your question(REQUIRED):
c) Why do I see (......)?
Why do I get an error instead of the comparison working? This is an ubuntu system (so they use PicardCommandLine).
I get similar error with
PicardCommandLine CompareSAMs script_A1_hisat2_alignments.sam shell_A1_hisat2_alignments.sam LENIENT_HEADER=true
which gives
========
INFO 2020-09-01 20:10:57 CompareSAMs
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
**********
********** The command line looks like this in the new syntax:
**********
********** CompareSAMs script_A1_hisat2_alignments.sam shell_A1_hisat2_alignments.sam -LENIENT_HEADER true
**********
ERROR: Unrecognized option: LENIENT_HEADER
USAGE: CompareSAMs [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CompareSAMs
Compare two input ".sam" or ".bam" files. This tool initially compares the headers of SAM or BAM files. If the file
headers are comparable, the tool will examine and compare readUnmapped flag, reference name, start position and strand
between the SAMRecords. The tool summarizes information on the number of read pairs that match or mismatch, and of reads
that are missing or unmapped (stratified by direction: forward or reverse).
Usage example:
java -jar picard.jar CompareSAMs \
file_1.bam \
file_2.bam
Version: 2.18.25
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
TMP_DIR=File One or more directories with space available to be used by this program for temporary
storage of working files Default value: null. This option may be specified 0 or more
times.
VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to
clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG}
QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can
be set to 'null' to clear the default value. Possible values: {true, false}
VALIDATION_STRINGENCY=ValidationStringency
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This
option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT,
SILENT}
COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
This option can be set to 'null' to clear the default value.
MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 500000.
This option can be set to 'null' to clear the default value.
CREATE_INDEX=Boolean Whether to create a BAM index when writing a coordinate-sorted BAM file. Default value:
false. This option can be set to 'null' to clear the default value. Possible values:
{true, false}
CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. This option can be set to 'null' to clear the default value. Possible values:
{true, false}
REFERENCE_SEQUENCE=File
R=File Reference sequence file. Default value: null.
GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json.
This option can be set to 'null' to clear the default value.
USE_JDK_DEFLATER=Boolean
USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. This option can be set to 'null' to clear the default value. Possible
values: {true, false}
USE_JDK_INFLATER=Boolean
USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. This option can be set to 'null' to clear the default value. Possible
values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
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Never mind
The debian/ubuntu version is just too old.
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Thank you for posting your solution, Uri David Akavia!
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